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Crystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with covalent inhibitor GR109
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G0M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.5 M AmSO4
1 M LiSO4
0.1 M Trisodium Citrate
Crystal Properties Matthews coefficient Solvent content 2.47 50.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.889 α = 90 b = 44.573 β = 97.599 c = 136.897 γ = 90
Symmetry Space Group I 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2019-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.911880 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.09 67.85 97.6 0.994 7.9 3.8 201068
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.09 1.11 0.803
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5g0m 1.09 42.383 200996 9956 97.342 0.173 0.1719 0.1817 0.1849 0.1948 11.154
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.334 0.162 0.366 -0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.827 r_dihedral_angle_1_deg 18.657 r_dihedral_angle_4_deg 15.322 r_dihedral_angle_3_deg 11.525 r_lrange_it 4.099 r_lrange_other 3.819 r_scangle_it 2.86 r_scangle_other 2.859 r_angle_refined_deg 1.991 r_scbond_it 1.948
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.827 r_dihedral_angle_1_deg 18.657 r_dihedral_angle_4_deg 15.322 r_dihedral_angle_3_deg 11.525 r_lrange_it 4.099 r_lrange_other 3.819 r_scangle_it 2.86 r_scangle_other 2.859 r_angle_refined_deg 1.991 r_scbond_it 1.948 r_scbond_other 1.948 r_angle_other_deg 1.692 r_mcangle_it 1.573 r_mcangle_other 1.573 r_mcbond_it 1.092 r_mcbond_other 1.089 r_symmetry_xyhbond_nbd_refined 0.281 r_nbd_refined 0.265 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.193 r_nbd_other 0.181 r_symmetry_nbd_refined 0.138 r_chiral_restr 0.115 r_xyhbond_nbd_refined 0.114 r_symmetry_nbtor_other 0.096 r_symmetry_xyhbond_nbd_other 0.033 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3323 Nucleic Acid Atoms Solvent Atoms 566 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing